Mocydia crocea
Info
| NCBI taxon id: | 592556 NCBI; ENA; GoaT |
|---|---|
| Order: | Hemiptera |
| Family: | Cicadellidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Auchenorrhyncha;Membracoidea;Cicadellidae;Deltocephalinae;Cicadulini;Mocydia; |
| GoaT genome size (M): | 4,658 (ancestor) |
| GoaT asm span (M): | 1,317 (ancestor) |
| GoaT chr no.: | 21 (ancestor) |
| GoaT haploid no.: | 9 (ancestor) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | ihMocCroe |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| ihMocCroe1 | Ox000341 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA8603337 | SAMEA8563713 |
| ihMocCroe2 | Ox001057 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA8603925 | SAMEA8603269 |
| ihMocCroe3 | NHMUK014444846 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | ABDOMEN | SAMEA115599728 | SAMEA115574653 |
| ihMocCroe4 | NHMUK014444844 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | ABDOMEN | SAMEA115599725 | SAMEA115574652 |
| ihMocCroe5 | NHMUK014444861 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | ABDOMEN | SAMEA115599699 | SAMEA115574639 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | ihMocCroe3 | 31 | 16.83 | 2,101,206,937 | 52.84 | 1.33 | 97.64 | 0.14 |   histogram.txt |
| hic-arima2 | ihMocCroe2 | 31 | 180.9 | 1,875,544,263 | 65.81 | 1.41 | 96.54 | 0.24 |   histogram.txt |
| pacbio | ihMocCroe1 | 31 | 8.794 | 2,007,981,319 | 53.13 | 1.60 | 98.97 | 0.18 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | ihMocCroe1 | 2021-06-22 | 83503 | m64230e_210622_180142 | D01 | 1022 | 18,101,901,496 | 17,455 | SAMEA8603337 | ||
| PacBio - HiFi | ihMocCroe1 | 2021-07-02 | 84025 | m64230e_210702_175202 | A01 | 1022 | 19,275,682,616 | 14,453 | SAMEA8603337 | ||
| PacBio - HiFi | ihMocCroe3 | 2025-03-14 | TRACTION-RUN-1818 | m84098_250314_153233_s3 | C01 | 2085 | 74,013,469,094 | 13,010 | SAMEA115599728 |
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Illumina run data
Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | ihMocCroe2 | 2023-10-16 | 47973_4#1 | 6,034,926,774 | 911,273,942,874 | SAMEA8603925 | qc complete |
Cobionts
Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.
identity | info |
|---|---|
| 0.989607 | NZ_CP016223.1 Candidatus Sulcia muelleri strain NC, complete genome |
| 0.97868 | [43 seqs] NZ_JQAM01000001.1 Wolbachia pipientis strain wRec s1, whole genome shotgun sequence [...] |
| 0.940539 | [20 seqs] NZ_JRLH01000001.1 Arsenophonus endosymbiont str. Hangzhou of Nilaparvata lugens strain Hangzhou contig1, whole genome shotgun sequence [...] |
| 0.936296 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.921343 | [256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...] |
| 0.913038 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.910933 | [833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...] |
| 0.909049 | [2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, complete genome [...] |
| 0.906067 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.905724 | NC_009987.1 Spiroplasma kunkelii virus SkV1_CR2-3x, complete genome |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.
specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
| No matching records found | ||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ihMocCroe1 |    |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
- Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
- FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
- Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
- Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
- Connections_Base: Number of Hi-C connections per base pair
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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